Implementation of affordable whole genome sequencing for front-line genomic analysis of Escherchia coli of veterinary and human importance

Project AbstractThe goal of this proposal is to obtain funding for the purchase and installation of the Illumina iSeq 100sequencing platform. This would include training on the iSeq workflow was well as Nextera DNA librarypreparation. Post installation and training, this proposal includes sequencing 10 E. coli isolates providedby a collaborating Vet-LIRN laboratory. In addition, this laboratory will be providing guidance andtraining on the Nextera Flex library kit and the workflow, which includes de novo assembly, read andassembly quality statistics, serotype prediction, AMR gene detection, and sequence type determination.The ultimate goal is to produce acceptable E. coli whole genome sequences to be analyzed using a user-friendly tool. This data will be used for both human and animal surveillance as well as on-farm herdmanagement decisions.